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During an investigation of a pre-warp alien planet, Reed accidentally leaves his communicator behind. When he returns with Archer to get the piece of technology, they are captured by soldiers who accuse them of being enemy spies.

The three look everywhere in the room, the launch bay and in the shuttlepod – it's definitely on the planet. Reed knows he used it at the beginning of the mission, but not at any other point. Sato suggests using the ship's scanners, and, indeed, she pinpoints it to a few buildings and they recognize the area. T'Pol stresses the importance of not contaminating a pre-warp culture, and Archer decides to head down with Reed to retrieve the communicator hoping it hasn't been found by someone else. During, Reed punishes himself but Archer notes it was just an accident.

At the tavern they had been before, they sit at the same table and are approached by the same bartender. He remembers them, and T'Pol, and suggests a certain food. They accept it so that he goes, but he discretely informs three people at another table that they are suspicious. Indeed, Reed tries to keep discrete in using a scanner, and finds the communicator in a room, obviously because someone found it. They go there, but it's locked and they need to wait for them to come out. However, this is the time that the three people get up and confront them. Archer starts a fight, but the two are soon subdued and brought in the back.

There, they find it was a trap set by the local military and are questioned. This time, a lot of technology is found on them, including a phase-pistol and scanners. The leader there, Pell, orders a message to a general named Gosis, believing he has found two enemy spies for an enemy faction called the Alliance.

Tucker gets frustrated, and thinks something is wrong. T'Pol agrees and sees the need to risk detection by hailing them. They don't respond, and Sato sees that they are a good deal away from the tavern. T'Pol orders Sato to isolate their bio-signs as best she can.

Archer and Reed have been brought to a detention center. Reed is further despondent on furthering the damage they've done. He considers telling them the truth, since their current belief is pretty dangerous. The man they met before comes to bring them to an interrogation by Gosis. It appears that he heard T'Pol's hail, and asks which of the two is "the captain." Archer answers it, and that they are not from the military, but no questions about the devices. Gosis suggests they were there to assassinate chancellorKultarey. While interrogating them, Archer is hit twice to the head, which damages the prosthetic and cuts him. When they see that their blood is red, Gosis orders they be taken to a doctor named Temec for a full examination.

On Enterprise, Sato identifies the compound the two are at and a plan is made to rescue the captain and Reed. Trip Tucker suggests using a Suliban cell ship to rescue them, but says that he will need a little time to get the cloaking device working. T'Pol agrees, and has Sato monitor communications in the meantime. While they try to identify the operation of the cloaking device, however, Tucker has a little accident in the process, and his forearm becomes cloaked.

Phlox tries to scan Tucker, but he can't get any information through the cloak. Tucker feels fine, just a little tingly. Phlox can only guess that he got a "long-term" dosage of whatever radiation the technology uses, and it will eventually regenerate on its own. He'll try scanning again in an hour. He brings him a glove and recommends a fresh uniform to work with.

On the planet, Gosis confronts Archer and Reed again, now with disturbing information that their internal organs are very different from their own. Furthermore, their surveillance has captured a picture of their shuttle and found it traveling at very high speed. Archer and Reed manage to explain their situation without going out of the local social context; they are spies, genetically enhanced prototypes and equipped with prototype devices as well. Gosis can't believe it, and has them taken back to the cell. Following that, Temec notes it's plausible and suggests killing them to study their enhanced organs in more detail.

Mayweather and Tucker continue to work on the cell ship, with only steady progress. When she learns of the execution plan, T'Pol decides to rush things a little and Trip has to finish his work on the cloak on their way to the planet. Meanwhile, back in their cell, Archer and Malcolm discuss the implications of their actions. Archer notes that T'Pol will certainly be able to retrieve the technology and their bodies when they are dead. The two briefly entertain the idea of telling the truth, but Archer concludes that it is the wrong choice, even at the expense of their lives. Reed assures Archer he isn't afraid to die, but also expects a rescue at any moment.

T'Pol, Mayweather and Tucker launch and are intercepted by three local aircraft when the warp power fails with transfer of power to weapons, apparently an automatic action by the ship. Mayweather does his best to steady the ship as Tucker fixes the problem and the ship cloaks again.

Meanwhile, Archer and Reed are taken to the hanging platform. Archer tries to plead for Reed's life, saying they don't need to kill them both, but Gosis doesn't respond and they're both taken up. They have the noose around their necks as everyone hears, but not sees, a ship descending. Tucker and T'Pol jump out, stunning several of the aliens and, through the firefight, are able to untie their crew. However, Archer must go back to get their equipment. He successfully does so, as their weapons easily subdue most of the aliens. Archer finally joins the crew in the cell ship and they take off. Only Gosis stands now, in disbelief at what he is seeing.

Back on the Enterprise, Archer and T'Pol have a conversation about the recent events in which they both conclude that they contaminated the civilization no matter what they tried, making the faction they had contact with believe that their enemies were far more advanced than they were. T'Pol also informs the captain she would not have expected them to sacrifice their lives to protect the inhabitants of the planet, suggesting that she is impressed by Archer's selflessness.

"Captain, my carelessness was inexcusable. I'm prepared for whatever reprimand you feel is appropriate."
"How about thirty years in the brig, or maybe a good flogging?"
"Sir."
"It was an accident, Malcolm. It could have happened to any of us."

- Reed and Archer

"You won't be seeing your friends in The Alliance for a long time."

- Pell

"We came down to retrieve my communicator. Now, we've lost two of them. Not to mention my phase-pistol and a pair of scanners!"

- Reed

"Visitors from another world? There's no way to know how they'd react."

"I ran every imaginable test. If I were to extract the organs, I could study them in more detail."
"You'll be in charge of the execution. I'll inform the prisoners."

- Temec, on Archer and Reed's biological "mutations" and Gosis, to Pell

"It might be helpful on movie night if you bring a date... (Tucker looks at him) In case you wanna steal some popcorn!"

- Mayweather, to Tucker on the advantages of having an invisible hand

"You don't have to leave technology behind to contaminate a culture."

- T'Pol

"Dr. Temec has a theory about where you come from. I found it hard to believe until I saw this; it was taken by one of our reconnaissance pilots early this morning. He said the craft was traveling at very high speed."
"None of the other planets in our system is capable of supporting life. Where do you come from?"
"Our scientists tell me it's unlikely a craft of this size could have traveled from another star system. They suspect a larger craft must be nearby, perhaps even orbiting our planet. TELL ME YOUR ORDERS! Have you made contact with The Alliance?"

The final draft of this episode's script was issued on 7 November2002. The script specified that, during the scene in which the Suliban cell ship first appears in this installment, Tucker and Mayweather had "been working for over an hour," and that the episode's penultimate scene, with Archer and T'Pol in the captain's ready room, was set "a day later" than the scene before it.

This episode explores the importance of not introducing technology to civilizations which are not yet warp-capable. This would eventually be adopted by the Federation as one of its highest laws, the Prime Directive, a topic, coincidentally, explained in "A Piece of the Action".

Somehow, the Suliban cloaking technology used to rescue Archer and Reed was lost to the Federation by the time of Kirk's USS Enterprise.